Java libaray/API for VCF file

[golharam]

Hi all,

Is there a Java library for VCF files as Picard is for SAM/BAM files?

A quick google search didn't turn anything up.

[nilshomer]

Hi all,

Is there a Java library for VCF files as Picard is for SAM/BAM files?

A quick google search didn't turn anything up.

http://vcftools.sourceforge.net/links.html

[golharam]

Unfortunately they are all not Java. GATK is Java, but GATK has some complexities I'm trying to avoid. I'm actually building a version similar to Picard, or at least shares the same infrastructure.

[nilshomer]

Perhaps you could talk to the Picard developers to see if they would want to add this support?